High Level of Structural Polymorphism Driven by Mobile Elements in the Hox Genomic Region of the Chaetognath Spadella cephaloptera

Abstract

Little is known about the relationships between genome polymorphism, mobile element dynamics, and population size among animal populations. The chaetognath species Spadella cephaloptera offers a unique perspective to examine this issue because they display a high level of genetic polymorphism at the population level. Here, we have investigated in detail the extent of nucleotide and structural polymorphism in a region harboring Hox1 and several coding genes and presumptive functional elements. Sequencing of several bacterial artificial chromosome inserts representative of this nuclear region uncovered a high level of structural heterogeneity, which is mainly caused by the polymorphic insertion of a diversity of genetic mobile elements. By anchoring this variation through individual genotyping, we demonstrated that sequence diversity could be attributed to the allelic pool of a single population, which was confirmed by detection of extensive recombination within the genomic region studied. The high average level of nucleotide heterozygosity provides clues of selection in both coding and noncoding domains. This pattern stresses how selective processes remarkably cope with intense sequence turnover due to substitutions, mobile element insertions, and recombination to preserve the integrity of functional landscape. These findings suggest that genome polymorphism could provide pivotal information for future functional annotation of genomes.

Extreme Mitogenomic Variation Without Cryptic Speciation in Chaetognaths

“…Spadella cephaloptera and the 37 Sagitta elegans individuals including all the individuals for which the entire mitogenome was sequenced. The primers employed were designed to specifically amplify L36a, one of the two ancient chaetognath specific duplicates of the L36 genes de-tected in S. cephaloptera [47]. Furthemore, for S. elegans and S. setosa fragments of 18S and 28S ribosomal RNA, and for Spadella cephaloptera of 18S ribosomal RNA were amplified using primers and protocols described in ref.…”

Extreme Mitogenomic Variation in Natural Populations of Chaetognaths

“…Previous studies examining the genetics of chaetognaths reported high levels of diversity and significant population structuring, but also revealed unusual patterns of mitochondrial evolution ( Kulagin et al 2014 ; Marlétaz et al 2008 , 2010 ; Miyamoto 2012 ; Miyamoto et al 2010b ; Peijnenburg et al 2004 , 2005, 2006 ). In this study, we focus on single populations of a benthic ( Spadella cephaloptera ) and two planktonic ( Sagitta elegans and Sagitta setosa ) chaetognaths from which we sampled a large number of inviduals ( table 1 ).…”

“…Transcriptomic studies revealed that chaetognath genomes underwent extensive gene duplication; many genes are transcribed in operons, often associated with trans-splicing ( Marlétaz et al 2008 ). The nuclear genome of chaetognaths also appears highly polymorphic, with widespread structural variation driven by mobile elements ( Marlétaz et al 2010 ). All chaetognaths are protandrous hermaphrodites with internal fertilization occurring while eggs are in the ovary.…”

Βιολογία Ανάπτυξης Εκτρεφόμενων Πλατυψάρων

“…Στη Drosophila melanogaster, έχει αποδειχτεί ότι η έκθεση σε αιθέρα επάγει την απώλεια της έκφρασης του γονιδίου ultrabithorax (ubx) εξαιτίας μιας αλληλομορφικής παραλλαγής (allelic variation) του γονιδίου (Akam, 1998;Gibson & Hogness, 1996;). Στα θαλάσσια είδη, όπως ο αχινός (Strongylocentratus purpuratus), το ασκιδιοειδές Ciona intestinalis, το κεφαλοχορδωτό Branchiostoma floridae, παρουσιάζουν υψηλή αλληλομορφική παραλλακτικότητα (allelic variation) στο γονιδίωμά τους (Marlétaz et al, 2010). Υψηλός πολυμορφισμός, στη μοναδική συστάδα (cluster) ομοιοτικών γονιδίων, εντοπίστηκε στο κεφαλοχορδωτό Branchiostoma floridae.…”